Selection-driven trait loss in independently evolved cavefish populations

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 3, 2023

Abstract Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found phenotypic convergence due to parallel genetic changes. This suggests substantial role for constraint and determinism evolution indicates certain mutations are more likely contribute evolution. Here we use whole genome resequencing the Mexican tetra, Astyanax mexicanus , investigate how selection has shaped repeated of both trait loss enhancement across independent cavefish lineages. We show on standing variation de novo substantially adaptation. Our findings provide empirical support hypothesis genes with larger mutational targets substrate indicate features cave environment may impact rate at which occur.

Language: Английский

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Population genomics of premature termination codons in cavefish with substantial trait loss

Molecular Biology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 21, 2025

Abstract Loss-of-function alleles are a pertinent source of genetic variation with the potential to contribute adaptation. Cave-adapted organisms exhibit striking loss ancestral traits such as eyes and pigment, suggesting that loss-of-function may play an outsized role in these systems. Here, we leverage 141 whole genome sequences evaluate evolutionary history adaptive single nucleotide premature termination codons (PTCs) Mexican tetra. We find cave populations contain significantly more PTCs at high frequency than surface populations. also occur frequently genes inherent relaxed constraint relative rest genome. Using SLiM simulate PTC evolution cavefish population, show smaller population size increased drift is sufficient account for observed increase without positive selection. CRISPR-Cas9, mutation one genes, pde6c, produces phenotypes tetra mimic cave-derived traits. Finally, identify small subset candidate populations, within selective sweeps, beneficial reduced energy expenditure, handful be adaptive. Overall, our work provides rare characterization across wild finds they have important phenotypes, contributing growing body literature showing through subterranean organisms.

Language: Английский

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Fantastic beasts and how to study them: rethinking experimental animal behavior

Journal of Experimental Biology, Journal Year: 2024, Volume and Issue: 227(4)

Published: Feb. 15, 2024

ABSTRACT Humans have been trying to understand animal behavior at least since recorded history. Recent rapid development of new technologies has allowed us make significant progress in understanding the physiological and molecular mechanisms underlying behavior, a key goal neuroethology. However, there is tradeoff when studying its biological mechanisms: common protocols laboratory are designed be replicable controlled, but they often fail encompass variability breadth natural behavior. This Commentary proposes framework 10 questions that aim guide researchers incorporating rich context into their experimental design or choosing study system. The cover overarching considerations can provide template for interspecies comparisons, enable develop studies model organisms unlock experiments our quest

Language: Английский

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Novel Husbandry Practices Result in Rapid Rates of Growth and Sexual Maturation Without Impacting Adult Behavior in the Blind Mexican Cavefish

Zebrafish, Journal Year: 2023, Volume and Issue: 20(2), P. 86 - 94

Published: April 1, 2023

Animal model systems are dependent on the standardization of husbandry protocols that maximize growth and reduce generation time. The Mexican tetra, Astyanax mexicanus, exists as eyed surface blind cave dwelling populations. opportunity for comparative approaches between independently evolved populations has led to rapid A. mexicanus a evolution biomedical research. However, slow inconsistent rate remains major limitation expanded application mexicanus. Fortunately, this temporal can be addressed through changes accelerate rates while maintaining optimal health outcomes. Here, we describe protocol produces in diet, feeding frequency, sorting progressive tank size. This produced robust decreased age sexual maturity comparison our previous protocol. To determine whether impacted behavior, tested fish exploration schooling assays. We found no difference behavior two groups, suggesting increased will not impact natural variation behavioral traits. Taken together, standardized development genetic model.

Language: Английский

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A new cave population of Astyanax mexicanus from Northern Sierra de El Abra, Tamaulipas, Mexico

Subterranean Biology, Journal Year: 2023, Volume and Issue: 45, P. 95 - 117

Published: March 6, 2023

The Astyanax genus represents an extraordinary example of phenotypic evolution, being their most extreme examples the blind and depigmented morphs, which have evolved from independent surface-dwelling lineages. Among cave organisms, cavefish is a prominent model system to study regressive evolution. Before this study, 34 populations were known for be inhabited by morph. majority those are distributed in Northeast México, at Sierra Madre Oriental (32 cavefish), three main areas: de Guatemala, El Abra, Micos, two Balsas basin state Guerrero, Mexico. In present we describe new population found 4.5 km Southward Pachón cave, northern Abra limestone. Refugio resurgence with mixed fish different levels troglomorphism, surface fish, resembling other hybrid within Abra. Based on mitochondrial DNA characterization 16S ribosomal sequence, could identify lineage population, was placed closely related “New Lineage”, sharing haplotypes (i.e. Arroyo Lagartos) populations, instead Central (e.g. Tinaja cave). gives additional evidence intricate history system, where migration, drift, selection shaped evolution morphs through episodes mexicanus history.

Language: Английский

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Revealing the genetic and molecular drivers behind golden and platinum coloration in barramundi (Lates calcarifer)

Aquaculture, Journal Year: 2024, Volume and Issue: 586, P. 740820 - 740820

Published: March 12, 2024

Coloration is an important trait in many aquaculture species, particularly when rare color phenotypes hold high economic value. The barramundi (Lates calcarifer) a valuable species across its Indo-Pacific range. wild-type (WT) skin of typically silver to bronze. However, occasional sightings golden (xanthic), platinum (white), panda (golden with black patches), and variants have been observed. Several these variants, such as the golden-colored fish, significant commercial interest. Nonetheless, genetic basis coloration remains poorly understood. In this study, transcriptomic differences between were analyzed understand molecular drivers colouration. Differential analysis RNA-seq count data for WT identified multiple Differentially Expressed Genes (DEG). Additionally, Weighted Gene Co-expression Network Analysis (WGCNA) 14 modules genes that exhibit common expression patterns are associated coloration. Notably, circadian cycle, tyrosine metabolism, xanthophore-associated genes, melanogenesis among top pathways exhibited morphs. Further gene within those revealed statistical variations. To confirm role oca2 golden-skinned barramundi, Protein-Protein Interaction (PPI) network was constructed using DEGs. PPI demonstrated direct interaction melanogenesis, genes. For phenotype, potential candidates discovered, namely myo5aa, mlpha, kif5b, which alteration pigment transporters responsible melanin, carotenoids, pteridine. These may play variant.

Language: Английский

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A Recessive oca2 Mutation Underlies Albinism in Xiphophorus fish

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

Oculocutaneous albinism (OCA) is a group of genetic disorders characterized by impaired melanin production, leading to reduced pigmentation in the skin, hair, and eyes. Xiphophorus , genus small freshwater fish, has been pivotal model organism disorder research, providing key findings pathways governing physiological pathological pigment cell biology. Leveraging well-established research framework provided we have identified spontaneously occurring phenotype swordtail fish hellerii . Genetic mapping albino showed that associated with recessive mutation oca2 gene. This discovery provides novel opportunity explore functions gene differentiation, synthesis, melanosome assembly transportation function amelanotic melanoma development.

Language: Английский

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Functions of thyroid hormone signaling in regulating melanophore, iridophore, erythrophore, and pigment pattern formation in spotted scat (Scatophagus argus)

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 27, 2025

Spotted scat, a marine aquaculture fish, has variable body color development stages during their ontogenesis. However, the regulatory mechanism of patterns formation was poorly understood. Thyroid hormones (TH) function as an important endocrine factor in regulating metamorphosis. In this study, exogenous thyroid 3,5,3′-L-triiodothyronine (T3) and its inhibitor thiourea (TU) were used to treat spotted scat juveniles metamorphosis stage (from 60 90 dpf). The molecular hormone signaling revealed, using micro-observation pigments cells distribution, colorimetric evaluation carotenoids concentration measurement by spectrophotometry, comparative transcriptome analysis. consisted whole black color, bar, red spots, final pattern formed through When treated with TU disrupt signaling, levels T3 T4 significantly decreased, melanophores numbers increased, well expression genes involved melanin synthesis melanophore differentiation (tyr, tyrp1, dct, mitf, pmel, oca2, slc24a5, erbb3) increased. Besides, associated pteridine metabolism (apod, pnpla2, rdh12, stard10, xdh, abca1, retsat, scarb1, rgs2, gch1) accumulation stimulated, when disrupted TU. On contrary, elevated T3, which could weaken skin redness reduce number spots melanophores, diameter larval erythrophores. Notably, unlike erythrophores, iridophore promoted hormones, gene related (fhl2-l, fhl2, ltk, id2a, alx4) guanine (gmps, hprt1, ppat, impdh1b) up-regulated after treatment, but they down-regulated treatment. Above results showed that might play critical roles regulation deposition, thereby affecting pigment (melanophores, iridophores erythrophores) patterns. mechanisms hyperthyroid hypothyroid on different different. Excess impact rearrangement cell cycle, resulting abnormalities scat. Meanwhile, excessed juvenile enhanced disruption hormone. stimulated hormones. These findings provide new insights for exploring help elucidate coloration, may also contribute selective breeding ornamental fish.

Language: Английский

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Oca2targeting using CRISPR/Cas9 in the Malawi cichlidAstatotilapia calliptera

Royal Society Open Science, Journal Year: 2022, Volume and Issue: 9(4)

Published: April 1, 2022

Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing role requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing Astatotilapia calliptera, a generalist cichlid remarkably diverse Lake Malawi radiation. By targeting oca2 required for melanin synthesis other vertebrate species, show efficient germline transmission. Gene edits include indels coding region, probably result non-homologous end joining, large deletion 3' untranslated region due to homology-directed repair. We find that knock-out A. calliptera lack melanin, which may be useful developmental imaging embryos studying colour pattern formation adults. As resembles presumed ancestor cichlids radiation, establishing genome this species will facilitate investigating speciation, adaptation diversification textbook

Language: Английский

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Evolved Loss of Sleep and Circadian Rhythms in Cavefish

Springer eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 133 - 157

Published: Jan. 1, 2024

Language: Английский

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